Does time matter in phylogeny? A perspective from the fossil record

Abstract

The role of time (i.e. taxa ages) in phylogeny has been a source of intense debate within palaeontology for decades and has not yet been resolved fully. The fossilised birth-death range process is a model that explicitly accounts for information about species through time. It presents a fresh opportunity to examine the role of stratigraphic data in phylogenetic inference of fossil taxa. Here, we apply this model in a Bayesian framework to an exemplar dataset of well-dated conodonts from the Late Devonian. We compare the results to those obtained using traditional unconstrained tree inference. We show that the combined analysis of morphology and stratigraphic data under the FBD range process reduces overall phylogenetic uncertainty, compared to unconstrained tree inference. We find that previous phylogenetic hypotheses based on parsimony and stratophenetics are closer to trees generated under the FBD range process. However, the results also highlight that irrespective of the inclusion of age data, a large amount of topological uncertainty will remain. Bayesian inference provides the most intuitive way to represent the uncertainty inherent in fossil datasets and new flexible models increase opportunities to refine hypotheses in palaeobiology.

Bayesian inference reveals a complex evolutionary history of belemnites

“…Although other fossil "belemnoid" coleoid groups are likely more closely related to the Belemnitida than aulacoceratids (e.g., Diplobelida, Belemnoteuthida), these do not have proper rostra (sensu Fuchs, 2012) and so do not contribute to the resolution of internal relationships of belemnites, whose phylogeny is here inferred based mostly on rostrum characters. For the vast majority of belemnites, the rostrum is the only known part (e.g., Hoffmann and Stevens, 2020) mimicking the situation for conodonts, where inferences of their phylogenetic relationships must also be based on conodont element data with few characters only (e.g., Donoghue, 2001;Guenser et al, 2021;Bai et al, 2022). Morphological data comes from several published sources and our own observations (Table 1).…”

TreeSearch: Morphological Phylogenetic Analysis in R

“…Notwithstanding scenarios that go beyond the limits of parsimony, such as the simultaneous incorporation of stratigraphic data and other prior knowledge (e.g. Guenser et al 2021), neither parsimony nor probabilistic methods consistently recover 'better' trees when gains in accuracy are balanced against losses in precision (M. R. Smith 2019a). Even if probabilistic methods may eventually be improved through the creation of more sophisticated models that better reflect the nature of morphological data Tarasov 2019Tarasov , 2022, parsimony analysis remains a useful tool -not only because treatments of inapplicable character states are presently available, but also because it facilitates a deeper understanding of the underpinning data by emphasizing the reciprocal relationship between a tree and the synapomorphies that it implies.…”

Identification of the mode of evolution in incomplete carbonate successions

“…This barrier is gradually overcome by methodological advances, such as the Fossilized Birth-Death Model (Stadler et al 2018), which allows incorporation of parameters specific to the fossil record, such as fossilization rate, sampling probability and age uncertainties of fossil occurrences (Barido-Sottani et al 2020; Warnock, Heath, and Stadler 2020; Wright et al 2022; Barido-Sottani et al 2023). Recently, there is renewed appreciation for the importance of fossils in phylogenetic reconstructions (Quental and Marshall 2010; Mitchell, Etienne, and Rabosky 2019; Mongiardino Koch, Garwood, and Parry 2021; Guenser et al 2021). These studies focus on the role of the morphological information provided by extinct taxa, but less on what a modern understanding of the physical structure of the geological record contributes to reconstructing evolutionary processes from fossil-bearing stratigraphic successions.…”

“…Recently, there is renewed appreciation for the importance of fossils in phylogenetic reconstructions (Quental and Marshall 2010;Mitchell, Etienne, and Rabosky 2019;Mongiardino Koch, Garwood, and Parry 2021;Guenser et al 2021). These studies focus on the role of the morphological information provided by extinct taxa, but less on what a modern understanding of the physical structure of the geological record contributes to reconstructing evolutionary processes from fossil-bearing stratigraphic successions.…”